6NF2

Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)
GSCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)
QSCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
CV-set_8e6nf2C1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
NV-set_8e6nf2N1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
VV-set_8e6nf2V1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
EV-set_8e6nf2E1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
JV-set_8e6nf2J1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
SV-set_8e6nf2S1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
AGP120_2nde6nf2A3 A: beta barrelsX: V1/V2 domain in HIV gp120 (From Topology)H: V1/V2 domain in HIV gp120 (From Topology)T: V1/V2 domain in HIV gp120F: GP120_2ndECOD (1.6)
AGP120_3rde6nf2A2 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: GP120_3rdECOD (1.6)
AGP120_1ste6nf2A1 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
GGP120_2nde6nf2G1 A: beta barrelsX: V1/V2 domain in HIV gp120 (From Topology)H: V1/V2 domain in HIV gp120 (From Topology)T: V1/V2 domain in HIV gp120F: GP120_2ndECOD (1.6)
GGP120_3rde6nf2G3 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: GP120_3rdECOD (1.6)
GGP120_1ste6nf2G2 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
QGP120_2nde6nf2Q3 A: beta barrelsX: V1/V2 domain in HIV gp120 (From Topology)H: V1/V2 domain in HIV gp120 (From Topology)T: V1/V2 domain in HIV gp120F: GP120_2ndECOD (1.6)
QGP120_3rde6nf2Q2 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: GP120_3rdECOD (1.6)
QGP120_1ste6nf2Q1 A: a+b two layersX: gp120 inner domain (From Topology)H: gp120 inner domain (From Topology)T: gp120 inner domainF: GP120_1stECOD (1.6)
BGP41_1ste6nf2B1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: GP41_1stECOD (1.6)
IGP41_1ste6nf2I1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: GP41_1stECOD (1.6)
RGP41_1ste6nf2R1 A: a+b duplicates or obligate multimersX: MPER trimer (From Topology)H: MPER trimer (From Topology)T: MPER trimerF: GP41_1stECOD (1.6)
DV-sete6nf2D1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
MV-sete6nf2M1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
UV-sete6nf2U1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
FV-set_3e6nf2F1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
KV-set_3e6nf2K1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
TV-set_3e6nf2T1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
HV-set_12e6nf2H1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_12ECOD (1.6)
OV-set_12e6nf2O1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_12ECOD (1.6)
WV-set_12e6nf2W1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_12ECOD (1.6)
LV-sete6nf2L1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
PV-sete6nf2P1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
XV-sete6nf2X1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
C, N, V
Fab VRC03 VH-CH1 Homo sapiens (human) IGHV1-2*02, IGHV1-46*04, IGHJ3*01, IGHJ3*02, IGHJ5*02, IGHJ6*01, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05, IGHG1*12, IGHG1*14, IGHG1*13, IGHG1*09, IGHG1*10, IGHG1*07, IGHG1*11 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202503-0)
E, J, S
Fab PGT122 VH-CH1 Homo sapiens (human) IGHV4-59*02, IGHJ3*01, IGHG1*03, IGHG1*08, IGHG1*06 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202503-0)
D, M, U
Fab VRC03 L-KAPPA Homo sapiens (human) IGKV3-11*01, IGKV3D-11*01, IGKV3D-11*03, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202503-0)
F, K, T
Fab PGT122 L-LAMBDA Homo sapiens (human) IGLV3-21*01, IGLV3-21*02, IGLJ3*02, IGLC3*03 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202503-0)
H, O, W
Fab 0PV-c.01 VH-CH1 Homo sapiens (human) IGHV4-61*01, IGHV4-61*08, IGHV4-4*08, IGHJ1*01, IGHG1*03, IGHG1*08, IGHG1*06 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202503-0)
L, P, X
Fab 0PV-c.01 L-KAPPA Homo sapiens (human) IGKV2-40*01, IGKV2D-40*01, IGKJ4*01, IGKJ4*02, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202503-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
E, J, S
Heavy ChainIGHV4 -envelope glycoprotein gp120SAbDab (2025-02-14)
D, M, U
Light ChainIGKV3 Kappaenvelope glycoprotein gp120SAbDab (2025-02-14)
H, O, W
Heavy ChainIGHV4 -envelope glycoprotein gp41SAbDab (2025-02-14)
L, P, X
Light ChainIGKV2 Kappaenvelope glycoprotein gp41SAbDab (2025-02-14)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, G, Q
PF00516Envelope glycoprotein GP120 (GP120)Envelope glycoprotein GP120The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein (Swiss:P01730) and a chemokine receptor on the cell s ...Domain
B, I, R
PF00517Retroviral envelope protein (GP41)Retroviral envelope protein- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C, N, V
VRC03 Heavy Chain---
E, J, S
PGT122 Heavy Chain---
A, G, Q
Envelope glycoprotein gp120
B, I, R
Envelope glycoprotein gp41
D, M, U
VRC03 Light Chain---
F, K, T
PGT122 Light Chain---
H, O, W
0PV-c.01 Heavy Chain---
L, P, X
0PV-c.01 Light Chain---